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- PDB-1mvf: MazE addiction antidote -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1mvf
TitleMazE addiction antidote
Components
  • PemI-like protein 1
  • immunoglobulin heavy chain variable region
KeywordsIMMUNE SYSTEM / plasmid addiction / camel antibody / addiction antidote
Function / homology
Function and homology information


toxin sequestering activity / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / double-stranded DNA binding / protein-containing complex binding / regulation of DNA-templated transcription / protein homodimerization activity / protein-containing complex / DNA binding
Similarity search - Function
: / Pemi-like Protein 1; Chain: D / Pemi-like Protein 1; Chain: D - #10 / SpoVT / AbrB like domain / Antidote-toxin recognition MazE, bacterial antitoxin / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / SpoVT-AbrB domain superfamily / Ribbon / Immunoglobulins ...: / Pemi-like Protein 1; Chain: D / Pemi-like Protein 1; Chain: D - #10 / SpoVT / AbrB like domain / Antidote-toxin recognition MazE, bacterial antitoxin / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / SpoVT-AbrB domain superfamily / Ribbon / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Antitoxin MazE / Antitoxin MazE
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLoris, R. / Marianovsky, I. / Lah, J. / Laeremans, T. / Engelberg-Kulka, H. / Glaser, G. / Muyldermans, S. / Wyns, L.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of the intrinsically flexible addiction antidote MazE.
Authors: Loris, R. / Marianovsky, I. / Lah, J. / Laeremans, T. / Engelberg-Kulka, H. / Glaser, G. / Muyldermans, S. / Wyns, L.
History
DepositionSep 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: immunoglobulin heavy chain variable region
B: immunoglobulin heavy chain variable region
D: PemI-like protein 1
E: PemI-like protein 1


Theoretical massNumber of molelcules
Total (without water)48,5164
Polymers48,5164
Non-polymers00
Water3,405189
1
A: immunoglobulin heavy chain variable region
E: PemI-like protein 1


Theoretical massNumber of molelcules
Total (without water)24,2582
Polymers24,2582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: immunoglobulin heavy chain variable region
D: PemI-like protein 1


Theoretical massNumber of molelcules
Total (without water)24,2582
Polymers24,2582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.440, 47.826, 128.376
Angle α, β, γ (deg.)90.000, 90.591, 90.000
Int Tables number4
Space group name H-MP1211
DetailsMazE-cabmaz1 complex. MazE is a dimer. Each MazE monomer has one monomer of cabmaz1 bound

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Components

#1: Antibody immunoglobulin heavy chain variable region


Mass: 14891.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli)
#2: Protein PemI-like protein 1 / MazE protein


Mass: 9366.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MazE / Production host: Escherichia coli (E. coli) / References: UniProt: P18534, UniProt: P0AE72*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, magnesium acetate, cacodylic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19 mg/mlprotein1drop
220 %PEG80001reservoir
30.1 Msodium cacodylate1reservoirpH6.5
40.2 Mmagnesium acetate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONEMBL/DESY, Hamburg BW7B10.87
SYNCHROTRONESRF ID14-320.9
Detector
TypeIDDetectorDateDetails
MARRESEARCH1IMAGE PLATEMar 21, 2001mirrors
ADSC QUANTUM 42CCDMar 10, 2002mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1mirrorsSINGLE WAVELENGTHMx-ray1
2mirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.871
20.91
ReflectionResolution: 1.65→15 Å / Num. obs: 32058 / % possible obs: 74.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.97 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 11.82
Reflection shellResolution: 1.65→1.75 Å / % possible all: 57.9
Reflection
*PLUS
Num. obs: 32375 / Num. measured all: 96388 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
Lowest resolution: 1.71 Å / % possible obs: 61 % / Num. unique obs: 2633 / Num. measured obs: 4348 / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 3.76

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2491 2575 random
Rwork0.2177 --
all0.2203 32058 -
obs0.2203 32058 -
Refinement stepCycle: LAST / Resolution: 1.65→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2489 0 0 189 2678
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.364
X-RAY DIFFRACTIONc_bond_d0.00605
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.36

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